Contacts of the helix formed by residues 90 - 103 (chain K) in PDB entry 1RQF
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 90 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29K TYR* 3.9 26.3 - - + +
86K ARG 3.7 11.2 - - - +
87K TYR* 2.8 23.5 + - - +
89K LEU* 1.3 81.4 - - + +
91K ASN* 1.3 65.4 + - - +
92K ARG* 3.5 8.0 + - - +
93K GLY 3.1 10.6 + - - -
94K ILE* 2.9 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 91 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89K LEU 4.0 0.4 + - - -
90K THR* 1.3 73.6 - - - +
92K ARG* 1.3 58.4 + - - +
94K ILE* 3.9 7.5 - - - +
95K ALA* 3.1 26.5 + - - +
166K MET* 5.8 1.0 - - - +
170K VAL* 3.9 29.1 - - + +
171K HIS* 5.6 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 92 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26K ASP* 2.8 28.1 + - - +
87K TYR* 2.9 24.9 - - + +
90K THR* 3.1 7.2 + - - +
91K ASN* 1.3 75.5 - - - +
93K GLY* 1.3 67.3 + - - +
95K ALA* 3.2 17.7 + - - +
96K GLN* 2.9 42.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 93 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23K CYS* 4.8 0.4 - - - -
87K TYR* 3.4 39.4 - - - -
88K ILE* 4.0 9.2 - - - -
90K THR* 3.0 10.1 + - - -
92K ARG* 1.3 77.7 - - - +
94K ILE* 1.3 62.3 + - - +
96K GLN* 2.9 15.7 + - - +
97K MET* 2.9 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 94 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88K ILE 3.2 21.7 + - - +
89K LEU* 3.6 6.3 - - - +
90K THR 2.9 16.1 + - - +
91K ASN* 3.9 6.7 - - - +
93K GLY* 1.3 74.8 - - - +
95K ALA* 1.3 58.0 + - - +
97K MET* 3.9 6.1 - - - +
98K LEU* 2.9 28.6 + - - +
163K PHE* 4.7 4.9 - - + -
166K MET* 3.4 41.1 - - + +
167K LEU* 4.1 17.9 - - + -
170K VAL* 3.7 16.8 - - + -
171K HIS* 3.7 30.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 95 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91K ASN 3.1 16.0 + - - +
92K ARG* 3.3 23.3 - - - +
93K GLY 3.1 0.2 - - - -
94K ILE* 1.3 77.8 - - - +
96K GLN* 1.3 61.9 + - - +
98K LEU* 3.4 8.7 + - - +
99K GLU* 3.2 19.6 + - - +
171K HIS* 5.0 7.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 96 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23K CYS* 4.3 11.6 - - + +
24K GLU* 3.0 33.7 + - - +
26K ASP* 3.7 2.6 + - - -
87K TYR* 2.4 38.6 + - - -
92K ARG* 2.9 37.6 - - - +
93K GLY 2.9 8.9 + - - +
95K ALA* 1.3 75.4 - - - +
97K MET* 1.3 64.1 + - - +
99K GLU* 3.0 22.4 - - - +
100K LYS* 3.2 13.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 97 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21K PHE 3.7 10.5 - - - +
23K CYS* 3.7 28.7 - - - -
84K HIS* 4.4 12.1 - - + -
88K ILE* 3.6 22.9 - - + -
93K GLY 2.9 13.6 + - - +
94K ILE 3.9 3.1 - - - +
96K GLN* 1.3 73.2 - - - +
98K LEU* 1.3 55.3 + - - +
100K LYS* 3.1 14.5 + - - +
101K TYR* 2.8 35.9 + - - +
106K PHE* 3.6 23.0 - - + -
121K PRO* 3.7 21.8 - - + -
159K PHE* 4.4 2.5 - - + -
163K PHE* 3.5 35.0 - - + -
167K LEU* 4.7 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 98 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94K ILE 2.9 18.4 + - - +
95K ALA* 3.5 7.4 - - - +
97K MET* 1.3 75.9 - - - +
99K GLU* 1.3 63.0 + - - +
101K TYR* 3.3 26.0 - - + +
102K GLN* 3.0 29.3 + - - +
167K LEU* 4.1 20.1 - - + +
171K HIS* 3.6 37.7 - - + +
174K TYR* 3.9 37.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 99 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95K ALA 3.2 11.1 + - - +
96K GLN* 3.0 16.0 + - - +
97K MET 3.0 0.2 - - - -
98K LEU* 1.3 77.1 - - - +
100K LYS* 1.3 66.0 + - + +
102K GLN* 2.9 30.7 + - - +
103K GLN* 2.6 50.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 100 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20K GLU 2.7 24.6 + - - -
21K PHE 4.3 0.7 - - - -
22K PHE 2.8 27.8 - - - +
23K CYS* 3.9 21.8 - - + +
96K GLN 3.4 10.1 - - - +
97K MET* 3.1 18.3 + - - +
99K GLU* 1.3 76.8 - - + +
101K TYR* 1.3 63.0 + - - +
103K GLN* 2.9 13.9 + - - -
105K ASP* 2.8 64.2 + - + +
106K PHE* 3.7 10.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 101 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97K MET 2.8 13.6 + - - +
98K LEU* 3.3 29.4 - - + +
100K LYS* 1.3 77.7 - - - +
102K GLN* 1.3 64.9 + - + +
104K GLY* 3.0 15.2 + - - +
105K ASP 5.0 0.2 - - - +
106K PHE* 3.7 8.2 - - - -
117K GLN* 2.8 23.6 + - - -
118K PRO* 3.3 44.2 - - + +
119K MET 3.6 8.3 - - - -
120K LEU* 3.4 40.6 - - + -
138K PRO* 3.6 9.0 - - - +
167K LEU* 5.4 1.6 - - + -
168K PHE* 4.0 9.0 - + - -
174K TYR* 4.3 30.8 + + + -
176K PRO* 4.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 102 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98K LEU* 3.0 25.0 + - + +
99K GLU* 2.9 31.9 + - - +
101K TYR* 1.3 80.3 - - + +
103K GLN* 1.3 69.0 + - - +
104K GLY 3.6 0.3 + - - -
174K TYR* 2.7 44.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 103 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99K GLU* 2.6 41.4 + - + +
100K LYS* 2.9 6.0 + - - +
102K GLN* 1.3 88.3 + - - +
104K GLY* 1.3 62.8 + - - +
105K ASP* 3.1 23.0 - - - +
108K TYR* 3.8 7.5 + - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il